This "Special Command," also known as the "Deportation Regime," originated with the illegal decree of 28 August 1941, ordering Soviet Germans in the Volga Republic region (but actually applied to all Germans) to be resettled farther east to prevent collaborating with the invading German army. As a peacetime special administration, the Spetskomandantura applied to all three categories of Soviet Germans and Mennonites: (1) local Germans (in the Orenburg settlements, etc.) who had not been uprooted; (2) those repatriated to the Soviet Union after 1945 (whose situation varied between [a] those scattered across the Soviet Union in labor camps, and [b] those placed in settled areas); and (3) those in the workers' army (Trud armia).

A secret administrative directive of 26 November 1948 finally clarified legal points of reference and administrative arrangements. Violations of the special command were punishable under sections 1a-d of Article 58, and also Article 19 of the Soviet Criminal Code. Within the Ministry of the Interior the Narodnyy komissariat vnutrennikh del (NKVD) established the Main Directorate of Deportations, which had an officer posted to every factory and office and a representative in every large town and village where the deported peoples lived.

There were four major implications for Mennonites and other Germans: (1) loss of all civil rights; (2) the splitting up of families, including the loss of many children to orphanages; (3) rigid controls on travel and correspondence, involving a special identity card and compulsory biweekly reporting (later monthly; annually after 1954); (4) loss of access to education, since they were outside the educational network. In that generation of children a large percentage grew up functionally illiterate. Until 1948, hunger was the major preoccupation, followed by inadequate housing, family separation concerns, and lack of educational access causing the loss of the German and Mennonite culture. After 1948 there were spiritual revivals in some of the Spetskomandantura camps, with Mennonites finding Christian fellowship with other Germans with whom they were thrown together.

The Spetskomandantura was abolished by decree in December 1955, with Soviet Germans and Mennonites receiving internal passports thereafter. The initial rehabilitation resulted in resumption of correspondence with loved ones, moving and family reunification, access to secondary schools and institutes, but also military service obligations. A further moral rehabilitation followed on 24 August 1964, and restrictions on moving back to the original home areas finally were lifted on 3 November 1972.